With Next-Generation Sequencing, MDx Catches Up to Antimicrobial Resistance

With Next-Generation Sequencing, MDx Catches Up to Antimicrobial Resistance

Market information and other trends regarding next-generation sequencing and healthcare-acquired infections are available through Kalorama Information reportsNext Generation Sequencing (NGS) Markets 2015andHealthcare Associated Infection (HAI) Control Markets.

A powerful tool for the development of now ubiquitous molecular infectious disease assays, sequencing is also capable of directly impacting clinical decision-making and disease control as an in vitro diagnostic (IVD).  Next generation sequencing’s emerging presence in the clinical lab is auspicious for the improved responsiveness of disease control in healthcare settings and personalization of individual patient therapy. While molecular diagnostics has revolutionized medicine, clinical demands are already stressing the capabilities of established molecular assays, including in the area of antimicrobial resistance and pathogen typing.

Primer and probe selection for molecular assays is a well-developed process, but such assays lack adaptability once in use in the majority of clinical labs. The fluid genetics of particularly virulent and antimicrobial-resistant strains and clones are at times capable of escaping the specificity of selected molecular probes and primers. NGS has demonstrated it can overcome other assays’ limitations; the technology features flexibility needed to widely detect any number of genetic variants.

Established molecular assay forms such as real-time PCR (qPCR) are able to overcome narrow analytical scope through multiplexed testing using panels. The benefit of multiplexed panels, particularly in the case of critical infections, is the positive identification of the infectious agent with shorter turnaround than repeat single-pathogen tests. Despite a widely-felt preference for larger assays, labs still point to drawbacks of larger panels that may include higher test product prices and undesirable selection of panel targets. Multiplexed molecular assays must often balance panel breadth with accuracy and clarity of results; false-positives can result from the inclusion of too many targets and sensitivity may be compromised.

Despite the success of multiplexed molecular assays, the inherent specificity of PCR and microarrays - still a competitive strength of molecular diagnostics over immunodiagnostics and traditional microbiology - can also prove to be a weakness, particularly in more complex application beyond detection such as genotyping and resistance profiling. Sequencing assays offer clinicians profound capabilities in accurate multiplexing without the same level of target definition required by other molecular assays and with rich results for clinical and epidemiological use.

Next-generation sequencing will not replace and has yet to compete with common molecular diagnostics such as PCR. The latter remains effective through syndromic panels that screen patients for common and likely pathogens based upon presented symptoms. The same multiplexed test or follow-up can additionally detect common resistance genes and established marker sequences for virulence and high-risk strains. However, the specificity of PCR assays makes them less suitable for clinical epidemiology and personalized medicine - two significant areas of health spending growth due to the unfortunate challenge of healthcare-acquired infections (HAIs).

Among the leaders in the NGS space for clinical infectious disease testing and antimicrobial resistance (AMR) surveillance is BioInnovation Solutions SA (formerly Pathogenica). The company’s CE-IVD HAI BioDetection Kit is multiplexed for the 12 most common nosocomial infections and 15 drug resistance genes. Otherwise, multiplexed HAI assay kits remain largely unavailable for the clinical market. The assay kit uses hundreds of probes to amplify loci of interest; the library of amplicons are subsequently sequenced and analyzed with a bioinformatics package. Sequencing results are referenced against databases for species, strains, sub-strains, and resistance genes. Approved for clinical diagnostic use in Europe, the HAI BioDetection Kit is an excellent representation of the duality and unique value of clinical sequencing - the kit can inform individual patient treatment but also serve as a tool for disease control and surveillance in a healthcare setting. The detailed results provided by the sequencing kit enable outbreak tracking through the identification of bacterial clones or distinct strains and sub-strains.

 Only a couple other diagnostics companies can currently offer standardized sequencing assays for infectious disease testing. Abbott Molecular offers its CE-IVD HBV sequencing assay for the determination of hepatitis B virus genotype and drug resistance prior to antiviral therapy. Singapore’s Vela Diagnostics offers a NGS workflow including system and research use-only (RUO) Sentosa NGS genotyping assay for HCV; Vela’s other Sentosa assays for oncology already have CE-IVD marking. However, the majority of NGS assays are available only as laboratory developed tests (LDTs) or testing services that do not require premarket approval or other clearance processes for clinical use otherwise required of test kits.

The above companies demonstrate the feasibility of introducing a standardized NGS assay kit to the market, but the relative scarcity of such products hints at ongoing regulatory uncertainty regarding the assessment of NGS. One bioinformatics company, PathoQuest, succinctly characterized the paradigm shift inherent to NGS that has stalled the introduction of further assay kits:

PathoQuest switches the search for the etiology of infectious diseases from a hypothesis-driven to a result-driven task, meaning your skills and resources can be fully dedicated to the interpretation of the results and treatment of the patient.

The market introduction and acceptance of NGS-based clinical diagnostics has at the same time been propelled by the technology’s unique capabilities and also held back from greater market development because of the challenges presented in assessing risk and suitable performance. With NGS diagnostics, the onus on the lab is shifted considerably from hypothesis-driven diagnosis to the interpretation of more data-rich results. In the case of infectious disease testing, the risk is considerable as it surpasses individual outcomes and could impact public health - and justifies careful deliberation on the part of the regulators and healthcare adopters.

Kalorama Information’s Next Generation Sequencing (NGS) Markets 2015 (Systems, Consumables, Services, Acquisitions, Agreements, Competitive Analysis, Platforms, Applications, Brand Ownership and Other Trends) comprehensively analyzes research and clinical markets for NGS as well as transformative iterations of the technology already edging into “third-generation sequencing” territory.